Alignment of IL_49714.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
Column number:
Node in JAR3D model:
Insertion positions indicated by I:
Position in motif group:		1
1
I

2
2

1
3
2
I

4
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
3
I

10
4

5
11
4
I

12
5


13
4
I

14
4

6
15
3
I

16
2

7
17
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
IL_49714.1_Instance_1 IL_49714.1,IL_3TZR_001,G52_C111GAACUACGC
IL_49714.1_Sequence_1 IL_49714.13TZR_G52_C111GAACUAC*GCtrue100000.00

Conserved interactions between motif group positions in IL_49714.1:
1 7 cWW 
2 3 s33 
3 5 perp 
4 5 s35 
4 7 cWS 
5 6 cWW 
6 7 s35 
5 3 7BPh
JAR3D SCFG/MRF model for IL_49714.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [7] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000076270135889769347254524013854470196433658662] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [7] | Norm Constant [0.249944093438588] // Cluster node 3TZR|1|A|G|52:3TZR|1|A|A|57 and 3TZR|1|B|C|111:3TZR|1|B|C|111
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3TZR|1|A|G|52 - 3TZR|1|B|C|111 cWW 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.201386650,0.228840829,0.201145128,0.197287187,0.000000000],[0.019558174,0.017360513,0.002189398,0.016922596,0.000000000],[0.018282593,0.002189398,0.054213877,0.009687809,0.000000000],[0.007930359,0.008467076,0.006745026,0.007793387,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3TZR|1|A|A|57 - 3TZR|1|B|C|111 cWS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3TZR|1|A|C|55
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 3TZR|1|A|U|56
Insertion    | Location [1] | Length Distribution [0.000000000,0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003781516,0.006781167,0.004347319,0.078825460,0.000000000],[0.056281056,0.026959555,0.589952696,0.038278585,0.000000000],[0.004396140,0.080523937,0.000828645,0.009304998,0.000000000],[0.079847353,0.005268669,0.010615539,0.004007366,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair C58 - G110 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from IL_49714.1:
> IL_49714.1  3TZR G   52 C  111
GAACUAC*GC